[BioC] flowCore: Prerequisites for norm2Filter?

[M. Jankowski]

Hi all,

Thank you all for your previous help. I really appreciate your assistance!

When I follow the HowTo I am able to apply the norm2Filter to the

> fs <- read.flowSet(path = system.file("extdata", "compdata", "data", package = "flowCore"), name.keyword = "SAMPLE ID", phenoData = list(name = "SAMPLE ID", Filename = "$FIL"))
> morphGate <- norm2Filter(filterId = "MorphologyGate", "FSC-H","SSC-H", scale = 2)
> smaller <- Subset(fs, morphGate)
>

However, the same sequence applied to my own data (see below) results
in a segfault. I can't figure out what I am doing wrong. Can anyone
help me out?

Thanks!
Matt

> fs =  read.flowSet(path="/home/mdj/data/NL10", patt="NL10\ control01.00*", alter.names=TRUE,phenoData = list(name = "SAMPLE ID", Filename = "$FIL"))
> morphGate <- norm2Filter(filterId = "MorphologyGate", "FSC.H","SSC.H", scale = 2)
> smaller <- Subset(fs, morphGate)

 *** caught segfault ***
address 0xa74e000, cause 'memory not mapped'

Traceback:
 1: .Fortran("rffastmcd", x, n, p, quan, nsamp, initcovariance =
initcov,     initmean = initmean, best = inbest, mcdestimate = deter,
   weights = weights, exactfit = fit, coeff = plane, kount = kount,
 adjustcov = adcov, seed, temp, index1, index2, nmahad, ndist,     am,
am2, slutn, med, mad, sd, means, bmeans, w, fv1, fv2,     rec, sscp1,
cova1, corr1, cinv1, cova2, cinv2, z, cstock,     mstock, c1stock,
m1stock, dath, cutoff, chimed, PACKAGE = "rrcov")
 2: .fastmcd(x, quan, nsamp, seed)
 3: covMcd(y)
 4: switch(table at method, covMcd = {    if (nrow(y) > table at n)
covMcd(y[sample(nrow(y), table at n), ])    else covMcd(y)}, cov.rob = {
  cov.rob(y)}, stop("How did you get here?"))
 5: x %in% subset
 6: x %in% subset

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: